Sodium in PDB 5c8w: Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp

All present enzymatic activity of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp:
2.7.11.12;

The structure of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp, PDB code: 5c8w was solved by J.C.Campbell, A.S.Reger, G.Y.Huang, B.Sankaran, J.J.Kim, C.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.73 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.710, 103.454, 176.405, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.6

The binding sites of Sodium atom in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp (pdb code 5c8w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp, PDB code: 5c8w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:20.4 occ:1.00 HE22 A:GLN198 2.4 20.0 1.0 HE22 B:GLN198 2.4 20.6 1.0 HB3 A:GLN217 2.9 16.7 1.0 HB3 B:GLN217 2.9 16.3 1.0 NE2 A:GLN198 3.2 16.7 1.0 NE2 B:GLN198 3.2 17.2 1.0 HE21 B:GLN198 3.6 20.6 1.0 HE21 A:GLN198 3.6 20.0 1.0 O A:HOH443 3.7 33.7 1.0 O B:HOH446 3.8 30.6 1.0 CB A:GLN217 3.9 13.9 1.0 CB B:GLN217 3.9 13.6 1.0 CD A:GLN198 4.2 15.4 1.0 CD B:GLN198 4.2 16.1 1.0 OE1 A:GLN198 4.2 18.7 1.0 OE1 B:GLN198 4.3 21.4 1.0 HB2 B:GLN217 4.3 16.3 1.0 HB2 A:GLN217 4.4 16.7 1.0 C A:GLN217 4.5 15.4 1.0 HG2 A:GLN217 4.5 16.4 1.0 HG2 B:GLN217 4.6 14.6 1.0 CA A:GLN217 4.6 12.8 1.0 C B:GLN217 4.6 18.2 1.0 CD B:GLN217 4.6 16.0 1.0 CG A:GLN217 4.6 13.7 1.0 HA A:GLN217 4.6 15.3 1.0 CG B:GLN217 4.6 12.1 1.0 CD A:GLN217 4.6 16.2 1.0 N A:GLY218 4.7 21.4 1.0 OE1 B:GLN217 4.7 17.7 1.0 H A:GLY218 4.7 25.7 1.0 CA B:GLN217 4.7 15.4 1.0 O A:GLN217 4.7 14.7 1.0 HA B:GLN217 4.7 18.4 1.0 OE1 A:GLN217 4.8 16.1 1.0 O B:GLN217 4.8 15.1 1.0 N B:GLY218 4.9 24.7 1.0 HA3 A:GLY218 5.0 33.5 1.0 H B:GLY218 5.0 29.6 1.0

Sodium binding site 2 out of 3 in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:28.3 occ:1.00 HE21 C:GLN198 2.4 26.0 1.0 HE22 E:GLN198 2.5 32.1 1.0 HB3 C:GLN217 2.9 34.5 1.0 HB3 E:GLN217 3.0 39.0 1.0 NE2 C:GLN198 3.2 21.6 1.0 NE2 E:GLN198 3.4 26.7 1.0 HE22 C:GLN198 3.6 26.0 1.0 HE21 E:GLN198 3.7 32.1 1.0 O C:HOH494 3.8 51.1 1.0 CB C:GLN217 3.8 28.8 1.0 CB E:GLN217 4.0 32.5 1.0 CD C:GLN198 4.2 19.3 1.0 CD E:GLN198 4.3 27.9 1.0 HB2 C:GLN217 4.3 34.5 1.0 HG2 C:GLN217 4.3 29.8 1.0 OE1 C:GLN198 4.4 27.7 1.0 OE1 E:GLN198 4.4 34.6 1.0 HB2 E:GLN217 4.4 39.0 1.0 C C:GLN217 4.4 27.4 1.0 HG2 E:GLN217 4.4 37.4 1.0 CG C:GLN217 4.5 24.9 1.0 CD E:GLN217 4.5 25.8 1.0 CG E:GLN217 4.5 31.1 1.0 CD C:GLN217 4.5 29.5 1.0 CA C:GLN217 4.6 25.6 1.0 OE1 E:GLN217 4.6 26.0 1.0 HA C:GLN217 4.6 30.8 1.0 OE1 C:GLN217 4.6 29.5 1.0 O C:GLN217 4.6 28.5 1.0 N C:GLY218 4.7 33.0 1.0 C E:GLN217 4.7 31.5 1.0 CA E:GLN217 4.8 25.8 1.0 HA E:GLN217 4.8 31.0 1.0 H C:GLY218 4.8 39.6 1.0 O E:HOH416 4.9 44.6 1.0 HA3 C:GLY218 4.9 49.4 1.0 NE2 E:GLN217 4.9 21.9 1.0 O E:GLN217 4.9 30.6 1.0

Sodium binding site 3 out of 3 in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na303 b:37.2 occ:1.00 HE21 F:GLN198 2.5 46.5 1.0 HB3 F:GLN217 2.9 33.2 1.0 NE2 F:GLN198 3.3 38.8 1.0 O F:HOH426 3.6 47.1 1.0 HE22 F:GLN198 3.7 46.5 1.0 CB F:GLN217 3.9 27.7 1.0 CD F:GLN198 4.3 45.1 1.0 C F:GLN217 4.3 41.6 1.0 OE1 F:GLN198 4.4 38.7 1.0 HB2 F:GLN217 4.4 33.2 1.0 HG2 F:GLN217 4.4 31.8 1.0 N F:GLY218 4.5 48.0 1.0 H F:GLY218 4.5 57.6 1.0 CA F:GLN217 4.5 27.9 1.0 HA F:GLN217 4.6 33.5 1.0 CG F:GLN217 4.6 26.5 1.0 O F:GLN217 4.6 30.5 1.0 CD F:GLN217 4.7 33.5 1.0 HA3 F:GLY218 4.7 69.9 1.0 OE1 F:GLN217 4.7 30.5 1.0

J.C.Campbell, J.J.Kim, K.Y.Li, G.Y.Huang, A.S.Reger, S.Matsuda, B.Sankaran, T.M.Link, K.Yuasa, J.E.Ladbury, D.E.Casteel, C.Kim. Structural Basis of Cyclic Nucleotide Selectivity in Cgmp-Dependent Protein Kinase II. J.Biol.Chem. V. 291 5623 2016.
ISSN: ESSN 1083-351X
PubMed: 26769964
DOI: 10.1074/JBC.M115.691303